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Crystal structure of GlmU in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 100mM Hepes (pH 7.5), 1mM DTT, 8% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.96 58.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.28 α = 90 b = 76.28 β = 90 c = 277.23 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH Varimax optics 2009-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.98 47.82 99.59 41778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 1.99 99.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DK5 1.98 47.82 41778 1048 99.59 0.16 0.1589 0.1607 0.2005 0.2041 RANDOM 31.3647
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 14.942 r_dihedral_angle_1_deg 7.073 r_scangle_it 5.438 r_scbond_it 3.483 r_angle_refined_deg 2.157 r_mcangle_it 2.117 r_mcbond_it 1.244 r_chiral_restr 0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_4_deg 19.792 r_dihedral_angle_3_deg 14.942 r_dihedral_angle_1_deg 7.073 r_scangle_it 5.438 r_scbond_it 3.483 r_angle_refined_deg 2.157 r_mcangle_it 2.117 r_mcbond_it 1.244 r_chiral_restr 0.255 r_bond_refined_d 0.027 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 74
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection PHASES phasing